The Joy of Computational Biology Nancy Griffeth

Outline What will we be doing Why I think computational biology is fun

Subject Matter Understanding how electrical activity in the heart relates to atrial fibrillation Workshop Information

Schedule This week: Introductory lectures (Staff) Next week: Advanced lectures (Fenton) Third week: Projects Last two days Team presentations Final visiting lecture Workshop Information>Schedule

Pedagogical Approach Collaborative Questions are always welcome Discussion is encouraged! Scribe to record unanswered questions Problem-oriented: Hodgkin-Huxley warm-up Spiral waves Workshop Information>Pedagogical Approach

Pedagogical Approach Interdisciplinary team oriented At least 1 biology expert At least 1 computer science expert At least 1 math expert Workshop Information>Pedagogical Approach

Speaking of Interdisciplinary… Workshop Information>Pedagogical Approach xkcd.com

General Learning Objectives Understand what excitable systems are Understand how chaotic behaviors arise in excitable systems Learn to function on interdisciplinary teams Investigate some research problems Meet new people and have some fun! Workshop Information>Pedagogical Approach

Specific Learning Objectives Learn what action potentials are, how they arise in cells, how they are propagated in cardiac tissue Understand how the propagation of action potentials relates atrial fibrillation Learn to understand models in the form of differential equations Create computer-processable models of cardiac cells Simulate their behavior Investigate their properties Project: Study formation of spiral waves of action potentials in cardiac tissue Workshop Information>Pedagogical Approach

Questions or Discussion?

What’s I like about comp bio Biology matters! Computational techniques help us understand biology Cells act a lot like computers Cells make binary choices Cells have modular parts Different kinds of cells share the same mechanisms Lots of good movies on-line

Computational techniques Organize data Describe behaviors as a whole Simulate behaviors Bridge gaps where data is missing Suggest hypotheses

Example 1: Cardiac Cells as Circuits K+ CMCM I(t) EKEK E Na ELEL gLgL gKgK g Na

Propagation of electrical signals across cardiac tissue

Example 2: Protein Production Transcription Figure from wikipedia article on the central dogma Transcription Translation

Protein Production Wiring diagrams Negative autoregulation: a protein represses its own production Provides a quick increase to a robust level

Protein Production cAMP signals absence of glucose cAMP activates X X binds to the DNA promoter, but is not enough by itself to start arabinose metabolism X promotes transcription of Y; arabinose activates Y X and Y together binding to the DNA promoter results in production of the enzymes that metabolize arabinose Figure from Alon, “An Introduction to Systems Biology”

What triggers activation of transcription factors? An external signal (molecule) arrives Binds to a receptor Changes in the receptor cause internal actions… Which cause cascading actions

Example 3: Regulating cell growth, proliferation, and differentiation

Example 4: Cell as Information Processor

Example 5: Protein degradation Ubiquitin Tags proteins for destruction Like garbage collection!!

Research Problems Atrial Fibrillation: alleviating the effects or curing the problem Computational complexity: how can we simplify the models enough to make them tractable?

Relationship to atrial fibrillation Electrical activity in the heart becomes chaotic Modeling the electrical activity helps us to understand how it develops Modeling can help us develop techniques or devices to prevent or alleviate it

Simplifying models Computationally complex Modular? Course-graining Need subsystems with behavior we can characterize

What you will learn… How action potentials work How action potentials relate to electrical activity in the heart Modeling with differential equations High-level view of how models can be “solved” numerically How spiral waves and chaotic activities start in cardiac tissue